env.yml

name: tahoeformer_env
channels:
  - pytorch
  - nvidia
  - bioconda
  - conda-forge
dependencies:
  - _openmp_mutex=4.5=3_kmp_llvm
  - alsa-lib=1.2.8=h166bdaf_0
  - argcomplete=3.6.2=pyhd8ed1ab_0
  - argh=0.31.3=pyhd8ed1ab_1
  - asttokens=3.0.0=pyhd8ed1ab_1
  - attr=2.5.1=h166bdaf_1
  - bcftools=1.17=h3cc50cf_1
  - biopython=1.85=py310ha75aee5_1
  - blas=1.0=mkl
  - brotli=1.1.0=hb9d3cd8_2
  - brotli-bin=1.1.0=hb9d3cd8_2
  - bzip2=1.0.8=h4bc722e_7
  - c-ares=1.34.5=hb9d3cd8_0
  - ca-certificates=2025.4.26=hbd8a1cb_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.16.0=ha61ee94_1014
  - certifi=2025.4.26=pyhd8ed1ab_0
  - comm=0.2.2=pyhd8ed1ab_1
  - contourpy=1.3.2=py310h3788b33_0
  - cpython=3.10.17=py310hd8ed1ab_0
  - cramjam=2.10.0=py310hed47299_0
  - cuda-cudart=12.1.105=0
  - cuda-cupti=12.1.105=0
  - cuda-libraries=12.1.0=0
  - cuda-nvrtc=12.1.105=0
  - cuda-nvtx=12.1.105=0
  - cuda-opencl=12.9.19=0
  - cuda-runtime=12.1.0=0
  - cuda-version=12.9=3
  - cudnn=9.9.0.52=h3828807_0
  - cycler=0.12.1=pyhd8ed1ab_1
  - dbus=1.13.6=h5008d03_3
  - debugpy=1.8.14=py310hf71b8c6_0
  - decorator=5.2.1=pyhd8ed1ab_0
  - exceptiongroup=1.2.2=pyhd8ed1ab_1
  - executing=2.2.0=pyhd8ed1ab_0
  - expat=2.7.0=h5888daf_0
  - fastparquet=2024.11.0=py310hf462985_0
  - fftw=3.3.10=nompi_hf1063bd_110
  - filelock=3.18.0=pyhd8ed1ab_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=h77eed37_3
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.57.0=py310h89163eb_0
  - freetype=2.12.1=h267a509_2
  - fsspec=2025.3.2=pyhd8ed1ab_0
  - gettext=0.24.1=h5888daf_0
  - gettext-tools=0.24.1=h5888daf_0
  - gffutils=0.13=pyh7cba7a3_0
  - glib=2.80.2=hf974151_0
  - glib-tools=2.80.2=hb6ce0ca_0
  - gmp=6.3.0=hac33072_2
  - gmpy2=2.2.1=py310he8512ff_0
  - graphite2=1.3.13=h59595ed_1003
  - gsl=2.7=he838d99_0
  - gst-plugins-base=1.21.3=h4243ec0_1
  - gstreamer=1.21.3=h25f0c4b_1
  - gstreamer-orc=0.4.41=h17648ed_0
  - h5py=3.9.0=nompi_py310h367e799_100
  - harfbuzz=6.0.0=h8e241bc_0
  - hdf5=1.14.0=nompi_h5231ba7_103
  - htslib=1.17=h6bc39ce_1
  - icu=70.1=h27087fc_0
  - importlib-metadata=8.6.1=pyha770c72_0
  - ipykernel=6.29.5=pyh3099207_0
  - ipython=8.36.0=pyh907856f_0
  - jack=1.9.22=h11f4161_0
  - jedi=0.19.2=pyhd8ed1ab_1
  - jinja2=3.1.6=pyhd8ed1ab_0
  - joblib=1.5.0=pyhd8ed1ab_0
  - jpeg=9e=h0b41bf4_3
  - jupyter_client=8.6.3=pyhd8ed1ab_1
  - jupyter_core=5.7.2=pyh31011fe_1
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.7=py310h3788b33_0
  - krb5=1.20.1=hf9c8cef_0
  - lame=3.100=h166bdaf_1003
  - lcms2=2.15=hfd0df8a_0
  - ld_impl_linux-64=2.43=h712a8e2_4
  - lerc=4.0.0=h0aef613_1
  - libaec=1.1.3=h59595ed_0
  - libasprintf=0.24.1=h8e693c7_0
  - libasprintf-devel=0.24.1=h8e693c7_0
  - libblas=3.9.0=16_linux64_mkl
  - libbrotlicommon=1.1.0=hb9d3cd8_2
  - libbrotlidec=1.1.0=hb9d3cd8_2
  - libbrotlienc=1.1.0=hb9d3cd8_2
  - libcap=2.66=ha37c62d_0
  - libcblas=3.9.0=16_linux64_mkl
  - libclang=15.0.7=default_h127d8a8_5
  - libclang13=15.0.7=default_h5d6823c_5
  - libcublas=12.1.0.26=0
  - libcufft=11.0.2.4=0
  - libcufile=1.14.0.30=4
  - libcups=2.3.3=h36d4200_3
  - libcurand=10.3.10.19=0
  - libcurl=7.87.0=h6312ad2_0
  - libcusolver=11.4.4.55=0
  - libcusparse=12.0.2.55=0
  - libdb=6.2.32=h9c3ff4c_0
  - libdeflate=1.17=h0b41bf4_0
  - libedit=3.1.20250104=pl5321h7949ede_0
  - libev=4.33=hd590300_2
  - libevent=2.1.10=h9b69904_4
  - libexpat=2.7.0=h5888daf_0
  - libffi=3.4.6=h2dba641_1
  - libflac=1.4.3=h59595ed_0
  - libgcc=14.2.0=h767d61c_2
  - libgcc-ng=14.2.0=h69a702a_2
  - libgcrypt=1.11.0=ha770c72_2
  - libgcrypt-devel=1.11.0=hb9d3cd8_2
  - libgcrypt-lib=1.11.0=hb9d3cd8_2
  - libgcrypt-tools=1.11.0=hb9d3cd8_2
  - libgettextpo=0.24.1=h5888daf_0
  - libgettextpo-devel=0.24.1=h5888daf_0
  - libgfortran=14.2.0=h69a702a_2
  - libgfortran-ng=14.2.0=h69a702a_2
  - libgfortran5=14.2.0=hf1ad2bd_2
  - libglib=2.80.2=hf974151_0
  - libgpg-error=1.55=h3f2d84a_0
  - libhwloc=2.9.1=hd6dc26d_0
  - libiconv=1.18=h4ce23a2_1
  - liblapack=3.9.0=16_linux64_mkl
  - libllvm15=15.0.7=hadd5161_1
  - libltdl=2.4.3a=h5888daf_0
  - libnghttp2=1.51.0=hdcd2b5c_0
  - libnpp=12.0.2.50=0
  - libnsl=2.0.1=hd590300_0
  - libnvjitlink=12.1.105=0
  - libnvjpeg=12.1.1.14=0
  - libogg=1.3.5=hd0c01bc_1
  - libopus=1.5.2=hd0c01bc_0
  - libpng=1.6.43=h2797004_0
  - libpq=15.1=h2baec63_3
  - libsndfile=1.2.2=hc60ed4a_1
  - libsodium=1.0.18=h36c2ea0_1
  - libsqlite=3.46.0=hde9e2c9_0
  - libssh2=1.10.0=haa6b8db_3
  - libstdcxx=14.2.0=h8f9b012_2
  - libstdcxx-ng=14.2.0=h4852527_2
  - libsystemd0=252=h2a991cd_0
  - libtiff=4.5.0=h6adf6a1_2
  - libtool=2.5.4=h5888daf_0
  - libudev1=253=h0b41bf4_0
  - libuuid=2.38.1=h0b41bf4_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp-base=1.5.0=h851e524_0
  - libxcb=1.13=h7f98852_1004
  - libxcrypt=4.4.36=hd590300_1
  - libxkbcommon=1.5.0=h79f4944_1
  - libxml2=2.10.3=hca2bb57_4
  - libzlib=1.2.13=h4ab18f5_6
  - llvm-openmp=15.0.7=h0cdce71_0
  - lz4-c=1.9.4=hcb278e6_0
  - markupsafe=3.0.2=py310h89163eb_1
  - matplotlib=3.9.1=py310hff52083_1
  - matplotlib-base=3.9.1=py310hf02ac8c_2
  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
  - mkl=2022.2.1=h84fe81f_16997
  - mpc=1.3.1=h24ddda3_1
  - mpfr=4.2.1=h90cbb55_3
  - mpg123=1.32.9=hc50e24c_0
  - mpmath=1.3.0=pyhd8ed1ab_1
  - munkres=1.1.4=pyh9f0ad1d_0
  - mysql-common=8.0.32=h14678bc_0
  - mysql-libs=8.0.32=h54cf53e_0
  - ncurses=6.5=h2d0b736_3
  - nest-asyncio=1.6.0=pyhd8ed1ab_1
  - networkx=3.4.2=pyh267e887_2
  - nspr=4.36=h5888daf_0
  - nss=3.100=hca3bf56_0
  - numpy=1.26.4=py310hb13e2d6_0
  - ocl-icd=2.3.3=hb9d3cd8_0
  - opencl-headers=2024.10.24=h5888daf_0
  - openjpeg=2.5.0=hfec8fc6_2
  - openssl=1.1.1w=hd590300_0
  - pandas=2.2.3=py310h5eaa309_3
  - parso=0.8.4=pyhd8ed1ab_1
  - patsy=1.0.1=pyhd8ed1ab_1
  - pcre2=10.43=hcad00b1_0
  - perl=5.32.1=7_hd590300_perl5
  - pexpect=4.9.0=pyhd8ed1ab_1
  - pickleshare=0.7.5=pyhd8ed1ab_1004
  - pillow=9.4.0=py310h023d228_1
  - pip=25.1.1=pyh8b19718_0
  - pixman=0.46.0=h29eaf8c_0
  - platformdirs=4.3.7=pyh29332c3_0
  - ply=3.11=pyhd8ed1ab_3
  - prompt-toolkit=3.0.51=pyha770c72_0
  - psutil=7.0.0=py310ha75aee5_0
  - pthread-stubs=0.4=hb9d3cd8_1002
  - ptyprocess=0.7.0=pyhd8ed1ab_1
  - pulseaudio=16.1=h4ab2085_1
  - pure_eval=0.2.3=pyhd8ed1ab_1
  - pygments=2.19.1=pyhd8ed1ab_0
  - pyparsing=3.2.3=pyhd8ed1ab_1
  - pyqt=5.15.7=py310hab646b1_3
  - pyqt5-sip=12.11.0=py310heca2aa9_3
  - pysam=0.21.0=py310hff46b53_0
  - python=3.10.8=h257c98d_0_cpython
  - python-dateutil=2.9.0.post0=pyhff2d567_1
  - python-tzdata=2025.2=pyhd8ed1ab_0
  - python_abi=3.10=7_cp310
  - pytorch=2.5.1=py3.10_cuda12.1_cudnn9.1.0_0
  - pytorch-cuda=12.1=ha16c6d3_6
  - pytorch-mutex=1.0=cuda
  - pytz=2025.2=pyhd8ed1ab_0
  - pyvcf3=1.0.3=pyhdfd78af_0
  - pyyaml=6.0.2=py310h89163eb_2
  - pyzmq=26.2.0=py310h71f11fc_1
  - qhull=2020.2=h434a139_5
  - qt-main=5.15.6=h18908ee_6
  - readline=8.2=h8c095d6_2
  - samtools=1.18=hd87286a_0
  - scikit-learn=1.6.1=py310h27f47ee_0
  - scipy=1.15.2=py310h1d65ade_0
  - seaborn=0.13.2=hd8ed1ab_3
  - seaborn-base=0.13.2=pyhd8ed1ab_3
  - setuptools=80.1.0=pyhff2d567_0
  - simplejson=3.20.1=py310ha75aee5_0
  - sip=6.7.12=py310hc6cd4ac_0
  - six=1.17.0=pyhd8ed1ab_0
  - stack_data=0.6.3=pyhd8ed1ab_1
  - statsmodels=0.14.4=py310hf462985_0
  - tbb=2021.9.0=hf52228f_0
  - threadpoolctl=3.6.0=pyhecae5ae_0
  - tk=8.6.13=noxft_h4845f30_101
  - toml=0.10.2=pyhd8ed1ab_1
  - tomli=2.2.1=pyhd8ed1ab_1
  - torchtriton=3.1.0=py310
  - tornado=6.4.2=py310ha75aee5_0
  - traitlets=5.14.3=pyhd8ed1ab_1
  - typing_extensions=4.13.2=pyh29332c3_0
  - tzdata=2025b=h78e105d_0
  - unicodedata2=16.0.0=py310ha75aee5_0
  - wcwidth=0.2.13=pyhd8ed1ab_1
  - wheel=0.45.1=pyhd8ed1ab_1
  - xcb-util=0.4.0=h516909a_0
  - xcb-util-image=0.4.0=h166bdaf_0
  - xcb-util-keysyms=0.4.0=h516909a_0
  - xcb-util-renderutil=0.3.9=h166bdaf_0
  - xcb-util-wm=0.4.1=h516909a_0
  - xkeyboard-config=2.38=h0b41bf4_0
  - xorg-kbproto=1.0.7=hb9d3cd8_1003
  - xorg-libice=1.1.2=hb9d3cd8_0
  - xorg-libsm=1.2.6=he73a12e_0
  - xorg-libx11=1.8.4=h0b41bf4_0
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-renderproto=0.11.1=hb9d3cd8_1003
  - xorg-xextproto=7.3.0=hb9d3cd8_1004
  - xorg-xproto=7.0.31=hb9d3cd8_1008
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - zeromq=4.3.5=h59595ed_1
  - zipp=3.21.0=pyhd8ed1ab_1
  - zlib=1.2.13=h4ab18f5_6
  - zstd=1.5.6=ha6fb4c9_0
  - pip:
      - accelerate==1.6.0
      - aiohappyeyeballs==2.6.1
      - aiohttp==3.11.18
      - aiosignal==1.3.2
      - annotated-types==0.7.0
      - arrow==1.3.0
      - async-timeout==5.0.1
      - attrs==21.4.0
      - binaryornot==0.4.4
      - chardet==5.2.0
      - charset-normalizer==3.4.2
      - click==8.1.8
      - colorlog==6.9.0
      - cookiecutter==2.6.0
      - deprecation==2.1.0
      - discrete-key-value-bottleneck-pytorch==0.1.1
      - docker-pycreds==0.4.0
      - einops==0.8.1
      - einx==0.3.0
      - enformer-pytorch==0.8.10
      - frozendict==2.4.6
      - frozenlist==1.6.0
      - future==1.0.0
      - gitdb==4.0.12
      - gitpython==3.1.44
      - huggingface-hub==0.30.2
      - idna==3.10
      - kipoi==0.8.6
      - kipoi-conda==0.3.1
      - kipoi-utils==0.7.7
      - kipoiseq==0.7.1
      - lightning==2.5.1.post0
      - lightning-utilities==0.14.3
      - markdown-it-py==3.0.0
      - mdurl==0.1.2
      - multidict==6.4.3
      - natsort==8.4.0
      - ncls==0.0.68
      - packaging==24.2
      - polars==1.29.0
      - propcache==0.3.1
      - protobuf==6.30.2
      - pydantic==2.11.4
      - pydantic-core==2.33.2
      - pyfaidx==0.8.1.4
      - pyranges==0.1.4
      - python-slugify==8.0.4
      - pytorch-lightning==2.5.1.post0
      - rdkit-pypi==2022.9.5
      - regex==2024.11.6
      - related==0.7.3
      - requests==2.32.3
      - rich==14.0.0
      - safetensors==0.5.3
      - sentry-sdk==2.27.0
      - setproctitle==1.3.6
      - smmap==5.0.2
      - sorted-nearest==0.0.39
      - sympy==1.13.1
      - tabulate==0.9.0
      - text-unidecode==1.3
      - tinydb==4.8.2
      - tokenizers==0.21.1
      - torchmetrics==1.7.1
      - tqdm==4.67.1
      - transformers==4.51.3
      - types-python-dateutil==2.9.0.20241206
      - typing-inspection==0.4.0
      - urllib3==2.4.0
      - vector-quantize-pytorch==1.22.16
      - wandb==0.19.10
      - yarl==1.20.0